Perspective on high-throughput bioanalysis to support in vitro assays in early drug discovery

As the desire for a shortened design/make/test/learn cycle increases in early drug discovery, the pressure to rapidly deliver drug metabolism pharmacokinetic data continues to rise. From a bioanalytical standpoint, in vitro assays are challenging because they are amenable to automation and thus capable of generating a high number of samples for analysis. To keep up with analysis demands, automated method development workflows, rapid sample analysis approaches and efficient data analysis software must be utilized. This work provides an outline of how we implemented those three aspects to provide bioanalytical support for in vitro drug metabolism pharmacokinetic assays, which include developing hundreds of mass spectrometry methods and analyzing thousands of samples per week, while delivering a median bioanalytical turnaround time of 1-2 business days.

High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives

For nearly two decades mass spectrometry has been used as a label-free, direct-detection method for both functional and affinity-based screening of a wide range of therapeutically relevant target classes. Here, we present an overview of several established and emerging mass spectrometry platforms and summarize the unique strengths and performance characteristics of each as they apply to high-throughput screening. Multiple examples from the recent literature are highlighted in order to illustrate the power of each individual technique, with special emphasis given to cases where the use of mass spectrometry was found to be differentiating when compared with other detection formats. Indeed, as many of these examples will demonstrate, the inherent strengths of mass spectrometry-sensitivity, specificity, wide dynamic range, and amenability to complex matrices-can be leveraged to enhance the discriminating power and physiological relevance of assays included in screening cascades. It is our hope that this review will serve as a useful guide to readers of all backgrounds and experience levels on the applicability and benefits of mass spectrometry in the search for hits, leads, and, ultimately, drugs.

Acoustic Ejection/Full-Scan Mass Spectrometry Analysis for High-Throughput Compound Quality Control

High-throughput analysis of compound dissolved in DMSO and arrayed in multiwell plates for quality control (QC) purposes has widespread utility in drug discovery, ranging from the QC of assay-ready plates dispatched by compound management, to compound integrity check in the screening collection, to reaction monitoring of chemical syntheses in microtiter plates. Due to the large number of samples (thousands per batch) involved, these workflows can put a significant burden on the liquid chromatography-mass spectrometry (LC-MS) platform typically used. To achieve the required speed of seconds per sample, several chromatography-free MS approaches have previously been used with mixed results. In this study, we demonstrated the feasibility of acoustic ejection-mass spectrometry (AE-MS) in full-scan mode for high-throughput compound QC in miniaturized formats, featuring direct, contactless liquid sampling, minimal sample consumption, and ultrafast analytical speed. The sample consumption and analysis time by AE-MS represent, respectively, a 1000-fold and 30-fold reduction compared with LC-MS. In qualitative QC, AE-MS generated comparable results to conventional LC-MS in identifying the presence and absence of expected compounds. AE-MS also demonstrated its utility in relative quantifications of the same compound in serial dilution plates, or substrate in chemical synthesis. To facilitate the processing of a large amount of data generated by AE-MS, we have developed a data processing platform using commercially available tools. The platform demonstrated fast and straightforward data extraction, reviewing, and reporting, thus eliminating the need for the development of custom data processing tools. The overall AE-MS workflow has effectively eliminated the analytical bottleneck in the high-throughput compound QC work stream.

Current status and future directions of high-throughput ADME screening in drug discovery

During the last decade high-throughput in vitro absorption, distribution, metabolism and excretion (HT-ADME) screening has become an essential part of any drug discovery effort of synthetic molecules. The conduct of HT-ADME screening has been "industrialized" due to the extensive development of software and automation tools in cell culture, assay incubation, sample analysis and data analysis. The HT-ADME assay portfolio continues to expand in emerging areas such as drug-transporter interactions, early soft spot identification, and ADME screening of peptide drug candidates. Additionally, thanks to the very large and high-quality HT-ADME data sets available in many biopharma companies, in silico prediction of ADME properties using machine learning has also gained much momentum in recent years. In this review, we discuss the current state-of-the-art practices in HT-ADME screening including assay portfolio, assay automation, sample analysis, data processing, and prediction model building. In addition, we also offer perspectives in future development of this exciting field.

Comparison of a High-Throughput Mass Spectrometry Method and Radioactive Filter Binding to Assay the Protein Methyltransferase PRMT5

Conformational remodeling of chromatin in cells is known to alter gene expression. The histone code hypothesis postulates that multiple modifications present on histone tails can regulate gene expression both through direct effects on chromatin compaction as well as through recruitment of unique complexes that signal specific downstream functions. Histone methylation is an important component of the histone code, and the dysregulation of histone methylation in disease makes methyltransferases and demethylases viable targets for drug discovery. We developed a biochemical assay platform, which takes advantage of the fact that protein methyltransferases (PMTs) all utilize the cofactor S-Adenosyl-L-methionine (SAM) as the methyl donor. The platform utilizes the High-throughput Mass Spectrometry (MS) technology to measure SAM and the S-Adenosyl-L-homocysteine product in a label-free manner. The platform has all the advantages of a label-free system coupled with the benefit of substrate agnostic measurements making it an ideal setup for PMT biochemical studies and drug discovery. In addition, MS is ideally suited for detecting multiple modification events within the same substrate. The ability to adjust the detection to monitor the methyl acceptor product allows for real-time measurements of multiple product species simultaneously, a distinct advantage over other commonly used assay formats.

From low- to high-throughput analysis

The high throughput is routinely used for the first steps of drug development such as drug discovery screening and toxicity. However, for PK analysis of regulated studies, the requirements and difficulties to achieve high-throughput analysis are more demanding due to regulatory guidelines that are not needed for early steps of drug discovery. High-throughput analysis can be required for any drug type from small molecules to larger ones. Contract research organizations must be prepared to deliver the results associated to these studies in a fast turnaround. Herein, we will describe the challenges encountered by a laboratory in order to go from low- to high-throughput analysis.

Standardized workflows for increasing efficiency and productivity in discovery stage bioanalysis

Merck consolidated discovery stage bioanalytical functions into the Department of Pharmacokinetics, Pharmacodynamics & Drug Metabolism in 2007. Since then procedures and equipment used to provide important quantitative data to project teams have been harmonized and in many cases standardized. This approach has enabled movement of work across the network of laboratories and has resulted in a lean, flexible and efficient organization. The overall goal was to reduce time and resources spent on routine activities while creating time to perform research in new areas and technologies to support future scientific needs. The current state of discovery bioanalysis at Merck is discussed, including hardware and software platforms, workflow procedures and performance metrics. Examples of improved processes will be discussed for compound tuning, LC method development, analytical acceptance criteria, automated sample preparation, sample analysis platforms, data processing and data reporting.

A high-speed liquid chromatography/tandem mass spectrometry platform using multiplexed multiple-injection chromatography controlled by single software and its application in discovery ADME screening

RATIONALE

Multiplexed liquid chromatography (LC) coupled with multiple-injection-chromatogram acquisition has emerged as the method of choice for high-speed discovery bioanalysis, because it significantly reduces injection-to-injection cycle time while maintaining the chromatography quality. Historically, systems utilizing this approach had been custom built, and therefore relied on custom software tools to communicate with multiple vendor software for system control, which lacked transferability, flexibility and robustness.

METHODS

In this study, we refined a multiplexed bioanalytical system previously reported, by implementing open-deck auto-sampler manifold and multiple-injection-chromatogram acquisition, all on a commercially available system with single software control.

RESULTS

As a result of these improvements, the developed LC/tandem mass spectrometry (MS/MS) method on the system was nearly three times faster than the previous method, while demonstrating comparable analytical accuracy, precision and robustness. This system has been evaluated for in vitro ADME screening assays including metabolic stability, CYP inhibition and Caco-2. The biological data generated on the developed system displayed good correlation with those from the previous LC/MS/MS approaches.

CONCLUSIONS

The developed platform demonstrated applicability to the in vitro screening assays evaluated and has been successfully implemented to support the high-throughput metabolic stability assay, with a significantly improved bioanalytical throughput, capacity and data turnaround.